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Brūmele B, Serova E, Lupp A, Suija M, Mutso M, Kurg R. Cross-Reactivity of N6AMT1 Antibodies with Aurora Kinase A: An Example of Antibody-Specific Non-Specificity. Antibodies (Basel) 2024; 13:33. [PMID: 38804301 PMCID: PMC11130794 DOI: 10.3390/antib13020033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
Primary antibodies are one of the main tools used in molecular biology research. However, the often-occurring cross-reactivity of primary antibodies complicates accurate data analysis. Our results show that three commercial polyclonal antibodies raised against N-6 adenine-specific DNA methyltransferase 1 (N6AMT1) strongly cross-react with endogenous and recombinant mitosis-associated protein Aurora kinase A (AURKA). The cross-reactivity was verified through immunofluorescence, immunoblot, and immunoprecipitation assays combined with mass spectrometry. N6AMT1 and AURKA are evolutionarily conserved proteins that are vital for cellular processes. Both proteins share the motif ENNPEE, which is unique to only these two proteins. We suggest that N6AMT1 antibodies recognise this motif in N6AMT1 and AURKA proteins and exhibit an example of "specific" non-specificity. This serves as an example of the importance of controls and critical data interpretation in molecular biology research.
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Affiliation(s)
- Baiba Brūmele
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Evgeniia Serova
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Aleksandra Lupp
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Mihkel Suija
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Margit Mutso
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
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Mutso M, Brūmele B, Serova E, Väärtnõu F, Suija M, Kurg R. The methyltransferase N6AMT1 participates in the cell cycle by regulating cyclin E levels. PLoS One 2024; 19:e0298884. [PMID: 38394175 PMCID: PMC10889616 DOI: 10.1371/journal.pone.0298884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
The methyltransferase N6AMT1 has been associated with the progression of different pathological conditions, such as tumours and neurological malfunctions, but the underlying mechanism is not fully understood. Analysis of N6AMT1-depleted cells revealed that N6AMT1 is involved in the cell cycle and cell proliferation. In N6AMT1-depleted cells, the cell doubling time was increased, and cell progression out of mitosis and the G0/G1 and S phases was disrupted. It was discovered that in N6AMT1-depleted cells, the transcription of cyclin E was downregulated, which indicates that N6AMT1 is involved in the regulation of cyclin E transcription. Understanding the functions and importance of N6AMT1 in cell proliferation and cell cycle regulation is essential for developing treatments and strategies to control diseases that are associated with N6AMT1.
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Affiliation(s)
- Margit Mutso
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Baiba Brūmele
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Evgeniia Serova
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Fred Väärtnõu
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mihkel Suija
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Reet Kurg
- Institute of Technology, University of Tartu, Tartu, Estonia
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3
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Yao T, Liu J, Jin E, Liu Z, Li H, Che Q, Zhu T, Li D, Li W. Expanding the Structural Diversity of Drimentines by Exploring the Promiscuity of Two N-methyltransferases. iScience 2020; 23:101323. [PMID: 32659721 PMCID: PMC7358741 DOI: 10.1016/j.isci.2020.101323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/12/2020] [Accepted: 06/25/2020] [Indexed: 11/20/2022] Open
Abstract
Methylation is envisioned as a promising way to rationally improve key pharmacokinetic characteristics of lead compounds. Although diverse tailoring enzymes are found to be clustered with cyclodipeptide synthases (CDPSs) to perform further modification reactions on the diketopiperazine (DKP) rings generating complex DKP-containing compounds, so far, a limited number of methyltransferases (MTs) co-occurring with CDPS have been experimentally characterized. Herein, we deciphered the methylation steps during drimentines (DMTs) biosynthesis with identification and characterization of DmtMT2-1 (from Streptomyces sp. NRRL F-5123) and DmtMT1 (from Streptomyces youssoufiensis OUC6819). DmtMT2-1 catalyzes N4-methylation of both pre-DMTs and DMTs; conversely, DmtMT1 recognizes the DKP rings, functioning before the assembly of the terpene moiety. Notably, both MTs display broad substrate promiscuity. Their combinatorial expression with the dmt1 genes in different Streptomyces strains successfully generated eight unnatural DMT analogs. Our results enriched the MT tool-box, setting the stage for exploring the structural diversity of DKP derivatives for drug development. The methylation steps during drimentines biosynthesis were unraveled Two N-MTs with different regioselectivities were identified The substrate promiscuities of DmtMT1 and DmtMT2-1 were probed Combinatorial biosynthesis expanded the chemical space of drimentines
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Affiliation(s)
- Tingting Yao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Jing Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Enjing Jin
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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4
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Li ZW, Liang S, Ke Y, Deng JJ, Zhang MS, Lu DL, Li JZ, Luo XC. The feather degradation mechanisms of a new Streptomyces sp. isolate SCUT-3. Commun Biol 2020; 3:191. [PMID: 32332852 PMCID: PMC7181669 DOI: 10.1038/s42003-020-0918-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/30/2020] [Indexed: 01/08/2023] Open
Abstract
Feather waste is the highest protein-containing resource in nature and is poorly reused. Bioconversion is widely accepted as a low-cost and environmentally benign process, but limited by the availability of safe and highly efficient feather degrading bacteria (FDB) for its industrial-scale fermentation. Excessive focuses on keratinase and limited knowledge of other factors have hindered complete understanding of the mechanisms employed by FDB to utilize feathers and feather cycling in the biosphere. Streptomyces sp. SCUT-3 can efficiently degrade feather to products with high amino acid content, useful as a nutrition source for animals, plants and microorganisms. Using multiple omics and other techniques, we reveal how SCUT-3 turns on its feather utilization machinery, including its colonization, reducing agent and protease secretion, peptide/amino acid importation and metabolism, oxygen consumption and iron uptake, spore formation and resuscitation, and so on. This study would shed light on the feather utilization mechanisms of FDBs. Li et a. report a new Streptromyces isolate, SCUT-3 which can efficiently degrade feather into products with high amino acid content, useful as feed for plants, animals and microbes. Using multiple omics and other techniques, they report how SCUT-3 turns on its feather utilization machinery and suggest a number of expressed genes most likely implicated in feather degradation.
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Affiliation(s)
- Zhi-Wei Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, P. R. China
| | - Shuang Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, P. R. China
| | - Ye Ke
- Yingdong College of Life Sciences, Shaoguan University, Shaoguan, Guangdong, P. R. China
| | - Jun-Jin Deng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, P. R. China
| | - Ming-Shu Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, P. R. China
| | - De-Lin Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, P. R. China
| | - Jia-Zhou Li
- Zhanjiang Ocean Sciences and Technologies Research Co. LTD, Zhanjiang, Guangdong, P. R. China
| | - Xiao-Chun Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, P. R. China.
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Firrman J, Liu L, Zhang L, Arango Argoty G, Wang M, Tomasula P, Kobori M, Pontious S, Xiao W. The effect of quercetin on genetic expression of the commensal gut microbes Bifidobacterium catenulatum, Enterococcus caccae and Ruminococcus gauvreauii. Anaerobe 2016; 42:130-141. [PMID: 27742572 DOI: 10.1016/j.anaerobe.2016.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/07/2016] [Accepted: 10/10/2016] [Indexed: 11/27/2022]
Abstract
Quercetin is one of the most abundant polyphenols found in fruits and vegetables. The ability of the gut microbiota to metabolize quercetin has been previously documented; however, the effect that quercetin may have on commensal gut microbes remains unclear. In the present study, the effects of quercetin on the commensal gut microbes Ruminococcus gauvreauii, Bifidobacterium catenulatum and Enterococcus caccae were determined through evaluation of growth patterns and cell morphology, and analysis of genetic expression profiles between quercetin treated and non-treated groups using Single Molecule RNA sequencing via Helicos technology. Results of this study revealed that phenotypically, quercetin did not prevent growth of Ruminococcus gauvreauii, mildly suppressed growth of Bifidobacterium catenulatum, and moderately inhibited growth of Enterococcus caccae. Genetic analysis revealed that in response to quercetin, Ruminococcus gauvreauii down regulated genes responsible for protein folding, purine synthesis and metabolism. Bifidobacterium catenulatum increased expression of the ABC transport pathway and decreased metabolic pathways and cell wall synthesis. Enterococcus caccae upregulated genes responsible for energy production and metabolism, and downregulated pathways of stress response, translation and sugar transport. For the first time, the effect of quercetin on the growth and genetic expression of three different commensal gut bacteria was documented. The data provides insight into the interactions between genetic regulation and growth. This is also a unique demonstration of how RNA single molecule sequencing can be used to study the gut microbiota.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Liqing Zhang
- Virginia Tech College of Engineering, Department of Computer Science, 1425 S Main St., Blacksburg, VA, 24061, USA
| | - Gustavo Arango Argoty
- Virginia Tech College of Engineering, Department of Computer Science, 1425 S Main St., Blacksburg, VA, 24061, USA
| | - Minqian Wang
- Rutgers University, Department of Food Science, 65 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Peggy Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Masuko Kobori
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8642, Japan
| | - Sherri Pontious
- Department of Microbiology and Immunology, Temple University School of Medicine, 3400 North Broad Street, Philadelphia, USA
| | - Weidong Xiao
- Department of Microbiology and Immunology, Temple University School of Medicine, 3400 North Broad Street, Philadelphia, USA
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A SAM-dependent methyltransferase cotranscribed with arsenate reductase alters resistance to peptidyl transferase center-binding antibiotics in Azospirillum brasilense Sp7. Appl Microbiol Biotechnol 2014; 98:4625-36. [PMID: 24573606 DOI: 10.1007/s00253-014-5574-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 01/23/2014] [Accepted: 01/25/2014] [Indexed: 10/25/2022]
Abstract
The genome of Azospirillum brasilense harbors a gene encoding S-adenosylmethionine-dependent methyltransferase, which is located downstream of an arsenate reductase gene. Both genes are cotranscribed and translationally coupled. When they were cloned and expressed individually in an arsenate-sensitive strain of Escherichia coli, arsenate reductase conferred tolerance to arsenate; however, methyltransferase failed to do so. Sequence analysis revealed that methyltransferase was more closely related to a PrmB-type N5-glutamine methyltransferase than to the arsenate detoxifying methyltransferase ArsM. Insertional inactivation of prmB gene in A. brasilense resulted in an increased sensitivity to chloramphenicol and resistance to tiamulin and clindamycin, which are known to bind at the peptidyl transferase center (PTC) in the ribosome. These observations suggested that the inability of prmB:km mutant to methylate L3 protein might alter hydrophobicity in the antibiotic-binding pocket of the PTC, which might affect the binding of chloramphenicol, clindamycin, and tiamulin differentially. This is the first report showing the role of PrmB-type N5-glutamine methyltransferases in conferring resistance to tiamulin and clindamycin in any bacterium.
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The endosymbiont Amoebophilus asiaticus encodes an S-adenosylmethionine carrier that compensates for its missing methylation cycle. J Bacteriol 2013; 195:3183-92. [PMID: 23667233 DOI: 10.1128/jb.00195-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All organisms require S-adenosylmethionine (SAM) as a methyl group donor and cofactor for various biologically important processes. However, certain obligate intracellular parasitic bacteria and also the amoeba symbiont Amoebophilus asiaticus have lost the capacity to synthesize this cofactor and hence rely on its uptake from host cells. Genome analyses revealed that A. asiaticus encodes a putative SAM transporter. The corresponding protein was functionally characterized in Escherichia coli: import studies demonstrated that it is specific for SAM and S-adenosylhomocysteine (SAH), the end product of methylation. SAM transport activity was shown to be highly dependent on the presence of a membrane potential, and by targeted analyses, we obtained direct evidence for a proton-driven SAM/SAH antiport mechanism. Sequence analyses suggest that SAM carriers from Rickettsiales might operate in a similar way, in contrast to chlamydial SAM transporters. SAM/SAH antiport is of high physiological importance, as it allows for compensation for the missing methylation cycle. The identification of a SAM transporter in A. asiaticus belonging to the Bacteroidetes phylum demonstrates that SAM transport is more widely spread than previously assumed and occurs in bacteria belonging to three different phyla (Proteobacteria, Chlamydiae, and Bacteroidetes).
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Pustelny C, Brouwer S, Müsken M, Bielecka A, Dötsch A, Nimtz M, Häussler S. The peptide chain release factor methyltransferase PrmC is essential for pathogenicity and environmental adaptation of Pseudomonas aeruginosa PA14. Environ Microbiol 2012; 15:597-609. [PMID: 23278968 DOI: 10.1111/1462-2920.12040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 11/02/2012] [Indexed: 01/30/2023]
Abstract
Pseudomonas aeruginosa pathogenicity and its capability to adapt to multiple environments are dependent on the production of diverse virulence factors, controlled by the sophisticated quorum sensing (QS) network of P. aeruginosa. To better understand the molecular mechanisms that underlie this adaptation we searched for novel key regulators of virulence factor production by screening a PA14 transposon mutant library for potential candidates acting downstream of the unique 2-alkyl-4-quinolone (AQ) QS system of P. aeruginosa. We focused the work on a protein named HemK with high homology to PrmC of Escherichia coli displaying a similar enzymatic activity (therefore also referred to as PrmC). In this study, we demonstrate that PrmC is an S-adenosyl-l-methionine (AdoMet)-dependent methyltransferase of peptide chain release factors (RFs) essential for the expression of several virulence factors, such as pyocyanin, rhamnolipids and the type III-secreted toxin ExoT. Furthermore, the PA14_prmC mutant strain is unable to grow under anoxic conditions and has a significantly reduced pathogenicity in the infection model Galleria mellonella. Along with transcriptomic and proteomic analyses, the presented data indicate that the methylation of RFs in P. aeruginosa seems to have a global effect on cellular processes related to the virulence of this nosocomial pathogen.
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Affiliation(s)
- Christian Pustelny
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.
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Graille M, Figaro S, Kervestin S, Buckingham RH, Liger D, Heurgué-Hamard V. Methylation of class I translation termination factors: structural and functional aspects. Biochimie 2012; 94:1533-43. [PMID: 22266024 DOI: 10.1016/j.biochi.2012.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 01/07/2012] [Indexed: 12/23/2022]
Abstract
During protein synthesis, release of polypeptide from the ribosome occurs when an in frame termination codon is encountered. Contrary to sense codons, which are decoded by tRNAs, stop codons present in the A-site are recognized by proteins named class I release factors, leading to the release of newly synthesized proteins. Structures of these factors bound to termination ribosomal complexes have recently been obtained, and lead to a better understanding of stop codon recognition and its coordination with peptidyl-tRNA hydrolysis in bacteria. Release factors contain a universally conserved GGQ motif which interacts with the peptidyl-transferase centre to allow peptide release. The Gln side chain from this motif is methylated, a feature conserved from bacteria to man, suggesting an important biological role. However, methylation is catalysed by completely unrelated enzymes. The function of this motif and its post-translational modification will be discussed in the context of recent structural and functional studies.
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Affiliation(s)
- Marc Graille
- IBBMC, Université Paris-Sud 11, CNRS UMR8619, Orsay Cedex, F-91405, France.
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Identification and characterization of the Chlamydia trachomatis L2 S-adenosylmethionine transporter. mBio 2011; 2:e00051-11. [PMID: 21558433 PMCID: PMC3104491 DOI: 10.1128/mbio.00051-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Methylation is essential to the physiology of all cells, including the obligate intracellular bacterium Chlamydia. Nevertheless, the methylation cycle is under strong reductive evolutionary pressure in Chlamydia. Only Parachlamydia acanthamoebae and Waddlia chondrophila genome sequences harbor homologs to metK, encoding the S-adenosylmethionine (SAM) synthetase required for synthesis of SAM, and to sahH, which encodes the S-adenosylhomocysteine (SAH) hydrolase required for detoxification of SAH formed after the transfer of the methyl group from SAM to the methylation substrate. Transformation of a conditional-lethal ΔmetK mutant of Escherichia coli with a genomic library of Chlamydia trachomatis L2 identified CTL843 as a putative SAM transporter based on its ability to allow the mutant to survive metK deficiency only in the presence of extracellular SAM. CTL843 belongs to the drug/metabolite superfamily of transporters and allowed E. coli to transport S-adenosyl-L-[methyl-(14)C]methionine with an apparent K(m) of 5.9 µM and a V(max) of 32 pmol min(-1) mg(-1). Moreover, CTL843 conferred a growth advantage to a Δpfs E. coli mutant that lost the ability to detoxify SAH, while competition and back-transport experiments further implied that SAH was an additional substrate for CTL843. We propose that CTL843 acts as a SAM/SAH transporter (SAMHT) serving a dual function by allowing Chlamydia to acquire SAM from the host cell and excrete the toxic by-product SAH. The demonstration of a functional SAMHT provides further insight into the reductive evolution associated with the obligate intracellular lifestyle of Chlamydia and identifies an excellent chemotherapeutic target. IMPORTANCE Obligate intracellular parasites like Chlamydia have followed a reductive evolutionary path that has made them almost totally dependent on their host cell for nutrients. In this work, we identify a unique transporter of a metabolite essential for all methylation reactions that potentially bypasses the need for two enzymatic reactions in Chlamydia. The transporter, CTL843, allows Chlamydia trachomatis L2 to steal S-adenosylmethionine (SAM) from the eukaryotic host cytosol and to likely remove the toxic S-adenosylhomocysteine (SAH) formed when SAM loses its methyl group, acting as a SAM/SAH transporter (SAMHT). In addition to reflecting the adaptation of Chlamydia to an obligate intracellular lifestyle, the specific and central roles of SAMHT in Chlamydia metabolism provide a target for the development of therapeutic agents for the treatment of chlamydial infections.
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Binet R, Maurelli AT. The chlamydial functional homolog of KsgA confers kasugamycin sensitivity to Chlamydia trachomatis and impacts bacterial fitness. BMC Microbiol 2009; 9:279. [PMID: 20043826 PMCID: PMC2807437 DOI: 10.1186/1471-2180-9-279] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 12/31/2009] [Indexed: 12/22/2022] Open
Abstract
Background rRNA adenine dimethyltransferases, represented by the Escherichia coli KsgA protein, are highly conserved phylogenetically and are generally not essential for growth. They are responsible for the post-transcriptional transfer of two methyl groups to two universally conserved adenosines located near the 3'end of the small subunit rRNA and participate in ribosome maturation. All sequenced genomes of Chlamydia reveal a ksgA homolog in each species, including C. trachomatis. Yet absence of a S-adenosyl-methionine synthetase in Chlamydia, the conserved enzyme involved in the synthesis of the methyl donor S-adenosyl-L-methionine, raises a doubt concerning the activity of the KsgA homolog in these organisms. Results Lack of the dimethylated adenosines following ksgA inactivation confers resistance to kasugamycin (KSM) in E. coli. Expression of the C. trachomatis L2 KsgA ortholog restored KSM sensitivity to the E. coli ksgA mutant, suggesting that the chlamydial KsgA homolog has specific rRNA dimethylase activity. C. trachomatis growth was sensitive to KSM and we were able to isolate a KSM resistant mutant of C. trachomatis containing a frameshift mutation in ksgA, which led to the formation of a shorter protein with no activity. Growth of the C. trachomatis ksgA mutant was negatively affected in cell culture highlighting the importance of the methylase in the development of these obligate intracellular and as yet genetically intractable pathogens. Conclusion The presence of a functional rRNA dimethylase enzyme belonging to the KsgA family in Chlamydia presents an excellent chemotherapeutic target with real potential. It also confirms the existence of S-adenosyl-methionine - dependent methylation reactions in Chlamydia raising the question of how these organisms acquire this cofactor.
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Affiliation(s)
- Rachel Binet
- Department of Microbiology and Immunology, F, Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814-4799, USA.
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12
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Pannekoek Y, Huis in ‘t Veld R, Hopman CTP, Langerak AAJ, Speijer D, van der Ende A. Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis. FEMS Microbiol Lett 2009; 294:216-24. [PMID: 19374669 PMCID: PMC2734931 DOI: 10.1111/j.1574-6968.2009.01568.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 03/04/2009] [Indexed: 01/06/2023] Open
Abstract
Hfq is a highly conserved pleiotropically acting prokaryotic RNA-binding protein involved in the post-transcriptional regulation of many stress-responsive genes by small RNAs. In this study, we show that Hfq of the strictly human pathogen Neisseria meningitidis is involved in the regulation of expression of components involved in general metabolic pathways, iron metabolism and virulence. A meningococcal hfq deletion strain (H44/76Deltahfq) is impaired in growth in nutrient-rich media and does not grow at all in nutrient-limiting medium. The growth defect was complemented by expression of hfq in trans. Using proteomics, the expression of 28 proteins was found to be significantly affected upon deletion of hfq. Of these, 20 proteins are involved in general metabolism, among them seven iron-responsive genes. Two proteins (PilE, TspA) are involved in adherence to human cells, a step crucial for the onset of disease. One of the differentially expressed proteins, GdhA, was identified as an essential virulence factor for establishment of sepsis in an animal model, studied earlier. These results show that in N. meningitidis Hfq is involved in the regulation of a variety of components contributing to the survival and establishment of meningococcal disease.
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Affiliation(s)
- Yvonne Pannekoek
- Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical CenterAmsterdam, The Netherlands
| | - Robert Huis in ‘t Veld
- Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical CenterAmsterdam, The Netherlands
| | - Carla Th P Hopman
- Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical CenterAmsterdam, The Netherlands
| | - Ankie AJ Langerak
- Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical CenterAmsterdam, The Netherlands
| | - Dave Speijer
- Clinical Proteomics Facility, Department of Medical Biochemistry, Academic Medical CenterAmsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical CenterAmsterdam, The Netherlands
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Nie DS, Liu YB, Lu GX. Cloning and primarily function study of two novel putative N5-glutamine methyltransferase (Hemk) splice variants from mouse stem cells. Mol Biol Rep 2008; 36:2221-8. [PMID: 19116772 DOI: 10.1007/s11033-008-9437-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Accepted: 12/12/2008] [Indexed: 12/31/2022]
Abstract
Methylation is one of epigenetic mechanisms regulating gene expression. The methylation pattern is determined during embryogenesis and passed over to differentiating cells and tissues. Beginning with the ESTs which were highly expressed in undifferentiated human ES cells and using homology research in mouse dbEST database, we cloned two novel putative (N (5))-glutamine methyltransferase (Hemk) splice variants termed mHemk1 and mHemk2 (Genbank accession number AY456393 and AY583759). Sequence analysis revealed that mHemk1 and mHemk2 cDNAs are 1,792 bp and 1,696 bp in length respectively. The deduced proteins have 214 amino acid residues (mHemk1) and 138 residues (mHemk2) in length and both share significant homology with (N (5))-glutamine methyltransferase (Hemk proteins) in database. Northern blot and RT-PCR analysis showed that mHemk mRNAs were abundantly expressed in undifferentiated ES cells, testis and brain, weakly expressed in differentiated ES cells and kidney, and not expressed in muscle, heart, placenta, pancreas, lung and stomach. Immunohistochemical analysis further revealed that the protein was most abundant in undifferentiated ES cells. The green fluorescent protein produced by pEGFP-C3/mHemk1 was detected mainly in the nucleus of COS7 cell lines after 24 h post-transfection. RNA interference (RNAi)-mediated knock-down method was established. Cell cycle analysis suggests that the cell proliferation decreases after RNAi with mHemk1. In vitro bioactivity assay showed that no evidence for a DNA adenine-methyltransferase activity was detected. The accumulating functional information from Hemk homology proteins in bacteria and yeast suggests that it may be an uncharacterized new mammalian N(5)-glutamine methyltransferase.
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Affiliation(s)
- Dong-Song Nie
- Institute of Human Reproduction and Stem Cell Engineering, Central South University, 88 Xiangya Road, Changsha, 410078 Hunan, People's Republic of China
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Motohashi R, Yamazaki T, Myouga F, Ito T, Ito K, Satou M, Kobayashi M, Nagata N, Yoshida S, Nagashima A, Tanaka K, Takahashi S, Shinozaki K. Chloroplast ribosome release factor 1 (AtcpRF1) is essential for chloroplast development. PLANT MOLECULAR BIOLOGY 2007; 64:481-97. [PMID: 17450416 DOI: 10.1007/s11103-007-9166-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 03/20/2007] [Indexed: 05/08/2023]
Abstract
To study the functions of nuclear genes involved in chloroplast development, we systematically analyzed albino and pale green Arabidopsis thaliana mutants by use of the Activator/Dissociation (Ac/Ds) transposon tagging system. In this study, we focused on one of these albino mutants, designated apg3-1 (for a lbino or p ale g reen mutant 3). A gene encoding a ribosome release factor 1 (RF1) homologue was disrupted by the insertion of a Ds transposon into the APG3 gene; a T-DNA insertion into the same gene caused a similar phenotype (apg3-2). The APG3 gene (At3g62910) has 15 exons and encodes a protein (422-aa) with a transit peptide that functions in targeting the protein to chloroplasts. The amino acid sequence of APG3 showed 40.6% homology with an RF1 of Escherichia coli, and complementation analysis using the E. coli rf1 mutant revealed that APG3 functions as an RF1 in E. coli, although complementation was not successful in the RF2-deficient (rf2) mutants of E. coli. These results indicate that the APG3 protein is an orthologue of E. coli RF1, and is essential for chloroplast translation machinery; it was accordingly named AtcpRF1. Since the chloroplasts of apg3-1 plants contained few internal thylakoid membranes, and chloroplast proteins related to photosynthesis were not detected by immunoblot analysis, AtcpRF1 is thought to be essential for chloroplast development.
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Affiliation(s)
- Reiko Motohashi
- Faculty of Agriculture, University of Shizuoka, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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Klimasauskas S, Weinhold E. A new tool for biotechnology: AdoMet-dependent methyltransferases. Trends Biotechnol 2007; 25:99-104. [PMID: 17254657 DOI: 10.1016/j.tibtech.2007.01.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 11/15/2006] [Accepted: 01/12/2007] [Indexed: 11/26/2022]
Abstract
AdoMet-dependent methyltransferases catalyze highly specific methyl group transfers from the ubiquitous cofactor S-adenosyl-L-methionine to a multitude of biological targets in the cell. Recently, DNA methyltransferases have been used for the sequence-specific, covalent attachment of larger chemical groups to plasmid and bacteriophage DNA using two classes of synthetic AdoMet analogs. These synthetic cofactors, in combination with the myriad AdoMet-dependent methyltransferases available in nature, provide new molecular tools for precise, targeted functionalization and labeling of large natural DNAs and, in all likelihood, RNAs and proteins. This paves the way for numerous novel applications in the functional analysis of biological methylation, biotechnology and medical diagnostics.
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Affiliation(s)
- Saulius Klimasauskas
- Laboratory of Biological DNA Modification, Institute of Biotechnology, LT-02241 Vilnius, Lithuania.
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Vestergaard B, Sanyal S, Roessle M, Mora L, Buckingham RH, Kastrup JS, Gajhede M, Svergun DI, Ehrenberg M. The SAXS Solution Structure of RF1 Differs from Its Crystal Structure and Is Similar to Its Ribosome Bound Cryo-EM Structure. Mol Cell 2005; 20:929-38. [PMID: 16364917 DOI: 10.1016/j.molcel.2005.11.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 11/15/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
Bacterial class I release factors (RFs) are seen by cryo-electron microscopy (cryo-EM) to span the distance between the ribosomal decoding and peptidyl transferase centers during translation termination. The compact conformation of bacterial RF1 and RF2 observed in crystal structures will not span this distance, and large structural rearrangements of RFs have been suggested to play an important role in termination. We have collected small-angle X-ray scattering (SAXS) data from E. coli RF1 and from a functionally active truncated RF1 derivative. Theoretical scattering curves, calculated from crystal and cryo-EM structures, were compared with the experimental data, and extensive analyses of alternative conformations were made. Low-resolution models were constructed ab initio, and by rigid-body refinement using RF1 domains. The SAXS data were compatible with the open cryo-EM conformation of ribosome bound RFs and incompatible with the crystal conformation. These conclusions obviate the need for assuming large conformational changes in RFs during termination.
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Affiliation(s)
- Bente Vestergaard
- Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Copenhagen
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